Momcilo Perisic, former chief of staff of the Yugoslav army, under guard before hearing his sentence at The Hague. Photograph: Peter Dejong/Reuters

The Yugoslav war crimes tribunal has sentenced the former chief of the Yugoslav army to 27 years in prison for providing military aid to Bosnian Serb forces responsible for the Srebrenica massacre and for a deadly four-year campaign of shelling and sniping in Sarajevo.

The verdict on General Momcilo Perisic is the first time the United Nations court has convicted a civilian or military officer from Yugoslavia of war crimes in Bosnia, and underscores the Yugoslav army's support for the Serb rebels in Bosnia and Croatia who committed the worst atrocities of the Balkan conflicts in the 1990s.

The link between the disintegrating Yugoslav federation and Serb forces in the breakaway republics has been a matter of dispute and was the keystone of the trial in The Hague of Yugoslav president Slobodan Milosevic. That trial ended without a conclusion when Milosevic died in his cell in 2006 of a heart attack.

The former Yugoslavia is now divided into independent states that include Serbia, Bosnia and Croatia.

Perisic is a former Milosevic ally who remained Serbia's military chief until 2008 – three years after the Bosnian and Croatian wars ended. He turned against the dictator after the Bosnian war and warned Milosevic's regime against fomenting conflict in Kosovo, where fighting erupted after he left his post.

The UN judges convicted Perisic of charges of providing officers, troops, ammunition and logistical support to the rebel Serbs in Bosnia and Croatia, but acquitted him of allegations that he was directly responsible as a superior officer to the Bosnian Serbs commanded by General Ratko Mladic.

Presiding judge Bakone Moloto said evidence reflected Perisic's "inability to impose binding orders on General Mladic … who maintained a measure of independence throughout the war".

Mladic was caught and transferred to The Hague for trial in May, after 16 years as one of the tribunal's most wanted fugitives. He faces genocide charges for allegedly masterminding ethnic cleansing campaigns and the massacre in 2005 of 8,000 Muslim men in the UN-protected Srebrenica enclave, Europe's worst massacre since the second world war.

The judges said Perisic "knew that it was highly probable" Bosnian Serbs would kill, abuse and expel Bosnian Muslims after seizing control of Srebrenica, but that he could not "reasonably have foreseen" the extent of the massacre, and they acquitted him of aiding and abetting extermination in the enclave.

In setting the lengthy sentence, the judges noted, however, that Perisic continued to send aid to the Bosnian Serbs for months after the massacre.

Dusan Ignjatovic, who heads the Serbian office for co-operation with the tribunal, said it was very important for Serbia that Perisic was not held directly responsible for the Srebrenica genocide.

Serbia's defence minister, Dragan Sutanovac, expressed regret over the verdict. "It is an extremely harsh sentence. I expect an appeal," he said.

The court did convict Perisic of having direct control over Croat rebels who shelled the capital of Croatia, Zagreb, in May 1995, killing seven civilians and injuring dozens more.

But while the judges ruled Perisic did not exercise superior responsibility over Bosnian Serbs, they said he oversaw a well-structured and covert operation to send military aid from Belgrade to the rebel Serbs, including millions of bullets and thousands of artillery shells.

The ruling said the military aid "became more centralised, structured and co-ordinated during General Perisic's tenure".

In a majority verdict, the three-judge panel said Perisic's material support "had a substantial effect on the crimes" committed by Bosnian Serb forces.

The Yugoslav army paid salaries and pensions of top officers, including Mladic, despite their long record of committing war crimes, the court said.

"The crimes charged in this case were not perpetrated by rogue soldiers acting independently," the 573-page judgment said. "Rather, they were part of a lengthy campaign overseen by top [Bosnian Serb] officers on the Yugoslav army's payroll, including General Mladic."

Moloto issued a dissenting opinion, in which he argued that providing aid to the Bosnian Serbs "to wage war cannot and should not be equated with aiding and abetting" crimes they committed.

In a landmark 2007 ruling, the International Court of Justice cleared Serbia of genocide in Bosnia but said the country's former government should have stopped the 1995 slaughter of some 8,000 Muslims in Srebrenica.